[gmx-users] DEFORM option in gromacs

Hi all Can anyone help me with the DEFORM option in Gromacs to change the box values? -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] putting step wise constraints in energy minimization

On 2/14/20 2:21 PM, Sadaf Rani wrote: Dear Gromacs users I want to run energy minimization in steps first to remove clashes with ions, second keeping position of heavy atoms fixed and thirdly removing all constraints. How can I set this in mdp file for ions and protein atoms? What you're

Re: [gmx-users] problem while calculating order parameter

Thanks On Sat, Feb 15, 2020, 8:02 PM Justin Lemkul wrote: > > > On 2/15/20 4:50 AM, Devargya Chakraborty wrote: > > i want to calculate the order prameter between two carbon atom namrd C01 > > and C03 in my topology file but while calculating, i am getting the > > following error. > > gmx order

[gmx-users] Script for looping n simulations

Hello gromacs users, I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. Many thanks, Neena -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Script for looping n simulations

On 2/15/20 11:44 AM, Neena Susan Eappen wrote: Hello gromacs users, I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle. It's the same logic as in

Re: [gmx-users] problem while calculating order parameter

On 2/15/20 4:50 AM, Devargya Chakraborty wrote: i want to calculate the order prameter between two carbon atom namrd C01 and C03 in my topology file but while calculating, i am getting the following error. gmx order is designed to compute deuterium order parameters in alkyl chains. It

Re: [gmx-users] Trajectory optimization - 2 chains are separated

On 2/15/20 9:52 AM, Marwa Abd El Kader wrote: Dear Justin, I 've tried centering on one chain and the same problem still exists, any suggestions? If centering on one chain via trjconv -center -pbc mol does not yield dimers, then I suspect the two chains are not actually associated and

Re: [gmx-users] Trajectory optimization - 2 chains are separated

Dear Justin, I 've tried centering on one chain and the same problem still exists, any suggestions? On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul wrote: > > > On 2/14/20 2:48 AM, Marwa Abd El Kader wrote: > > Dear Justin, > > Would you please tell me how, give me an example code, because I'm a >

Re: [gmx-users] problem while calculating order parameter

I guess you have not made your index file correctly. It should contain only the group for which you will calculate the order parameter. On Sat, Feb 15, 2020 at 3:21 PM Devargya Chakraborty < devargyachakraborty@gmail.com> wrote: > i want to calculate the order prameter between two carbon

[gmx-users] problem while calculating order parameter

i want to calculate the order prameter between two carbon atom namrd C01 and C03 in my topology file but while calculating, i am getting the following error. Taking z axis as normal to the membrane Reading file nvt.tpr, VERSION 2019.1 (single precision) Using following groups: Groupname: System

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 190, Issue 31

> On Feb 15, 2020, at 10:44 AM, > gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit >